Skip CCR Main Navigation National Cancer Institute National Cancer Institute U.S. National Institutes of Health www.cancer.gov
CCR - For Our Staff| Home |

Our Science – Nicklaus Website

Marc C. Nicklaus, Ph.D.

Selected Publications

1)  Lagunin AA, Filimonov DA, Gloriozova TA, Tarasova OA, Zakharov AV, Guasch-Pamies L, Nicklaus MC, Poroikov VV.
Virtual Screening of Potential Anti-HIV Agents in Libraries of Commercially Available Organic Compounds (Russ.).
Chem. Pharm. J. (Moscow). 47: 3-21, 2013.
[Journal]
2)  Zakharov AV, Lagunin AA, Filimonov DA, Poroikov VV.
Quantitative prediction of antitarget interaction profiles for chemical compounds.
Chem. Res. Toxicol. 25: 2378-85, 2012.
[Journal]
3)  Weidlich IE, Filippov IV, Brown J, Kaushik-Basu N, Krishnan R, Nicklaus MC, Thorpe IF.
Inhibitors for the hepatitis C virus RNA polymerase explored by SAR with advanced machine learning methods.
Bioorg. Med. Chem. [Epub ahead of print], 2013.
[Journal]
4)  Peach ML, Zakharov AV, Liu R, Pugliese A, Tawa G, Wallqvist A, Nicklaus MC.
Computational tools and resources for metabolism-related property predictions. 1. Overview of publicly available (free and commercial) databases and software.
Future Med Chem. 4: 1907-32, 2012.
[Journal]
5)  Zakharov AV, Peach ML, Sitzmann M, Filippov IV, McCartney HJ, Smith LH, Pugliese A, Nicklaus MC.
Computational tools and resources for metabolism-related property predictions. 2. Application to prediction of half-life time in human liver microsomes.
Future Med Chem. 4: 1933-44, 2012.
[Journal]
6)  Muresan S, Sitzmann M, Southan C.
Mapping between databases of compounds and protein targets.
Methods Mol. Biol. 910: 145-64, 2012.
[Journal]
7)  Geczy T, Peach ML, El Kazzouli S, Sigano DM, Kang J, Valle CJ, Selezneva J, Woo W, Kedei N, Lewin NE, Garfield SH, Lim L, Mannan P, Marquez VE, Blumberg PM.
Molecular Basis for Failure of "Atypical" C1 Domain of Vav1 to Bind Diacylglycerol/Phorbol Ester.
J. Biol. Chem. 287: 13137-58, 2012.
[Journal]
8)  Sitzmann M, Weidlich IE, Filippov IV, Liao C, Peach ML, Ihlenfeldt WD, Karki RG, Borodina YV, Cachau RE, Nicklaus MC.
PDB ligand conformational energies calculated quantum-mechanically.
J Chem Inf Model. 52: 739-56, 2012.
[Journal]
9)  Yao Z, Xu Y, Zhang M, Jiang S, Nicklaus MC, Liao C.
Discovery of a novel hybrid from finasteride and epristeride as 5-alpha-reductase inhibitor.
Bioorg. Med. Chem. Lett. 21: 475-8, 2011.
[Journal]
10)  O'Boyle NM, Guha R, Willighagen EL, Adams SE, Alvarsson J, Bradley JC, Filippov IV, Hanson RM, Hanwell MD, Hutchison GR, James CA, Jeliazkova N, Lang AS, Langner KM, Lonie DC, Lowe DM, Pansanel J, Pavlov D, Spjuth O, Steinbeck C, Tenderholt AL, Theisen KJ, Murray-Rust P.
Open Data, Open Source and Open Standards in chemistry: The Blue Obelisk five years on.
J Cheminform. 3: 37, 2011.
[Journal]
11)  Liao C, Sitzmann M, Pugliese A, Nicklaus MC.
Software and resources for computational medicinal chemistry.
Future Med Chem. 3: 1057-85, 2011.
[Journal]
12)  Yun SM, Moulaei T, Lim D, Bang JK, Park JE, Shenoy SR, Liu F, Kang YH, Liao C, Soung NK, Lee S, Yoon DY, Lim Y, Lee DH, Otaka A, Appella E, McMahon JB, Nicklaus MC, Burke TR, Yaffe MB, Wlodawer A, Lee KS.
Structural and functional analyses of minimal phosphopeptides targeting the polo-box domain of polo-like kinase 1.
Nat. Struct. Mol. Biol. 18: 516, 2011.
[Journal]
13)  Liao C, Marchand C, Burke TR, Pommier Y, Nicklaus MC.
Authentic HIV-1 integrase inhibitors.
Future Med Chem. 2: 1107-22, 2010.
[Journal]
14)  Liao C, Nicklaus MC.
Computer tools in the discovery of HIV-1 integrase inhibitors.
Future Med Chem. 2: 1123-40, 2010.
[Journal]
15)  Druzhilovsky DS, Filimonov DA, Liao C, Peach ML, Nicklaus MC, Poroikov VV.
Computer-Assisted Search and Optimization of New Human Immunodeficiency Virus Integrase Inhibitors.
Biochem. (Moscow) Suppl. Ser. B: Biomed. Chem. 4: 59-67, 2010.
[Journal]
16)  Liao C, Park J, Bang JK, Nicklaus MC, Lee KS.
Exploring Potential Binding Modes of Small Drug-like Molecules to the Polo-Box Domain of Human Polo-like Kinase 1.
ACS Med Chem Lett. 1: 110-114, 2010.
[Journal]
17)  Weidlich IE, Dexheimer T, Marchand C, Antony S, Pommier Y, Nicklaus MC.
Inhibitors of human tyrosyl-DNA phospodiesterase (hTdp1) developed by virtual screening using ligand-based pharmacophores.
Bioorg. Med. Chem. 18: 182-9, 2010.
[Journal]
18)  Oku N, Takada K, Fuller RW, Wilson JA, Peach ML, Pannell LK, McMahon JB, Gustafson KR.
Isolation, structural elucidation, and absolute stereochemistry of enigmazole A, a cytotoxic phosphomacrolide from the Papua New Guinea marine sponge Cinachyrella enigmatica.
J. Am. Chem. Soc. 132: 10278-85, 2010.
[Journal]
19)  Keck GE, Poudel YB, Rudra A, Stephens JC, Kedei N, Lewin NE, Peach ML, Blumberg PM.
Molecular modeling, total synthesis, and biological evaluations of C9-deoxy bryostatin 1.
Angew. Chem. Int. Ed. Engl. 49: 4580-4, 2010.
[Journal]
20)  Park J, Soung N, Johmura Y, Kang YH, Liao C, Lee KH, Park CH, Nicklaus MC, Lee KS.
Polo-box domain: a versatile mediator of polo-like kinase function.
Cell Mol Life Sci. 67: 1957-70, 2010.
[Journal]
21)  Liao C, Park J, Jeong K, Nicklaus MC, Lee KS.
Probing Binding Modes of Small Molecule Inhibitors to the Polo-Box Domain of Human Polo-like Kinase 1.
ACS Med Chem Lett. 1: 110-114, 2010.
[Journal]
22)  Liao C, Nicklaus MC.
Tautomerism and Magnesium Chelation of HIV-1 Integrase Inhibitors: A Theoretical Study.
ChemMedChem. 5: 1053-66, 2010.
[Journal]
23)  Sitzmann M, Ihlenfeldt WD, Nicklaus MC.
Tautomerism in large databases.
J. Comput. Aided Mol. Des. 24: 521-51, 2010.
[Journal]
24)  Zeng X, Yin B, Hu Z, Liao C, Liu J, Li S, Li Z, Nicklaus MC, Zhou G, Jiang S.
Total synthesis and biological evaluation of largazole and derivatives with promising selectivity for cancers cells.
Org. Lett. 12: 1368-71, 2010.
[Journal]
25)  Moon HR, Siddiqui MA, Sun G, Filippov IV, Landsman NA, Lee YC, Adams KM, Barchi JJ, Deschamps JR, Nicklaus MC, Kelley JA, Marquez VE.
Using conformationally locked nucleosides to calibrate the anomeric effect: Implications for glycosyl bond stability.
Tetrahedron. 66: 6707-6717, 2010.
[Journal]
26)  Dexheimer TS, Gediya LK, Stephen AG, Weidlich I, Antony S, Marchand C, Interthal H, Nicklaus M, Fisher RJ, Njar VC, Pommier Y.
4-Pregnen-21-ol-3,20-dione-21-(4-bromobenzenesulfonate) (NSC 88915) and related novel steroid derivatives as tyrosyl-DNA phosphodiesterase (Tdp1) inhibitors.
J. Med. Chem. 52: 7122-31, 2009.
[Journal]
27)  Peach ML, Nicklaus MC.
Combining docking with pharmacophore filtering for improved virtual screening.
J Cheminform. 1: 1-13, 2009.
Full Text Article. [Journal]
28)  Liao C, Nicklaus MC.
Comparison of nine programs predicting pK(a) values of pharmaceutical substances.
J Chem Inf Model. 49: 2801-12, 2009.
[Journal]
29)  Peach ML, Tan N, Choyke SJ, Giubellino A, Athauda G, Burke TR, Nicklaus MC, Bottaro DP.
Directed Discovery of Agents Targeting the Met Tyrosine Kinase Domain by Virtual Screening.
J Med Chem. 52: 943-51, 2009.
[Journal]
30)  Jiang S, Liao C, Bindu L, Yin B, Worthy KW, Fisher RJ, Burke TR, Nicklaus MC, Roller PP.
Discovery of thioether-bridged cyclic pentapeptides binding to Grb2-SH2 domain with high affinity.
Bioorg. Med. Chem. Lett. 19: 2693-8, 2009.
[Journal]
31)  Choi WJ, Kim SE, Stephen AG, Weidlich I, Giubellino A, Liu F, Worthy KM, Bindu L, Fivash MJ, Nicklaus MC, Bottaro DP, Fisher RJ, Burke TR.
Identification of Shc Src homology 2 domain-binding peptoid-peptide hybrids.
J. Med. Chem. 52: 1612-8, 2009.
[Journal]
32)  Filippov IV, Nicklaus MC.
Optical structure recognition software to recover chemical information: OSRA, an open source solution.
J Chem Inf Model. 49: 740-3, 2009.
[Journal]
33)  Yun SM, Moulaei T, Lim D, Bang JK, Park JE, Shenoy SR, Liu F, Kang YH, Liao C, Soung NK, Lee S, Yoon DY, Lim Y, Lee DH, Otaka A, Appella E, McMahon JB, Nicklaus MC, Burke TR, Yaffe MB, Wlodawer A, Lee KS.
Structural and functional analyses of minimal phosphopeptides targeting the polo-box domain of polo-like kinase 1.
Nat. Struct. Mol. Biol. 16: 876-82, 2009.
[Journal]
34)  Ludek OR, Schroeder GK, Liao C, Russ PL, Wolfenden R, Marquez VE.
Synthesis and Conformational Analysis of Locked Carbocyclic Analogues of 1,3-Diazepinone Riboside, a High-Affinity Cytidine Deaminase Inhibitor.
J Org Chem. 74: 6212-23, 2009.
[Journal]
35)  Boyer PL, Vu BC, Ambrose Z, Julias JG, Warnecke S, Liao C, Meier C, Marquez VE, Hughes SH.
The Nucleoside Analogue D-carba T Blocks HIV-1 Reverse Transcription.
J Med Chem. 52: 5356-64, 2009.
[Journal]
36)  Barchi JJ, Karki RG, Nicklaus MC, Siddiqui MA, George C, Mikhailopulo IA, Marquez VE.
Comprehensive Structural Studies of 2',3'-Difluorinated Nucleosides: Comparison of Theory, Solution, and Solid State.
J Am Chem Soc. 130: 9048-57, 2008.
[Journal]
37)  Duan D, Sigano DM, Kelley JA, Lai CC, Lewin NE, Kedei N, Peach ML, Lee J, Abeyweera TP, Rotenberg SA, Kim H, Kim YH, El Kazzouli S, Chung JU, Young HA, Young MR, Baker A, Colburn NH, Haimovitz-Friedman A, Truman JP, Parrish DA, Deschamps JR, Perry NA, Surawski RJ, Blumberg PM, Marquez VE.
Conformationally constrained analogues of diacylglycerol. 29. Cells sort diacylglycerol-lactone chemical zip codes to produce diverse and selective biological activities.
J. Med. Chem. 51: 5198-220, 2008.
[Journal]
38)  Comin MJ, Vu BC, Boyer PL, Liao C, Hughes SH, Marquez VE.
D-(+)-iso-methanocarbathymidine: a high-affinity substrate for herpes simplex virus 1 thymidine kinase.
ChemMedChem. 3: 1129-34, 2008.
[Journal]
39)  Sitzmann M, Filippov IV, Nicklaus MC.
Internet resources integrating many small-molecule databases(1).
SAR QSAR Environ Res. 19: 1-9, 2008.
[Journal]
40)  Blumberg PM, Kedei N, Lewin NE, Yang D, Czifra G, Pu Y, Peach ML, Marquez VE.
Wealth of opportunity - the C1 domain as a target for drug development.
Curr Drug Targets. 9: 641-52, 2008.
[Journal]
41)  Marquez VE, Sun G, Siddiqui MA, Lee YC, Barchi JJ, Filippov IV, Landsman NA, Kelley JA.
What are the consequences of freezing the anomeric effect in nucleosides?.
Nucleic Acids Symp Ser (Oxf). 543-4, 2008.
[Journal]
42)  Choi Y, Pu Y, Peach ML, Kang JH, Lewin NE, Sigano DM, Garfield SH, Blumberg PM, Marquez VE.
Conformationally constrained analogues of diacylglycerol (DAG). 28. DAG-dioxolanones reveal a new additional interaction site in the C1b domain of PKC delta.
J. Med. Chem. 50: 3465-81, 2007.
[Journal]
43)  Kang SU, Choi WJ, Oishi S, Lee K, Karki RG, Worthy KM, Bindu LK, Nicklaus MC, Fisher RJ, Burke TR.
Examination of acylated 4-aminopiperidine-4-carboxylic acid residues in the phosphotyrosyl+1 position of Grb2 SH2 domain-binding tripeptides.
J. Med. Chem. 50: 1978-82, 2007.
[Journal]
44)  Sun G, Nicklaus MC.
Natural Resonance Structures and Aromaticity of the Nucleobases.
Theor. Chem. Acc. 117: 323-332, 2007.
[Journal]
45)  Comin MJ, Agbaria R, Ben-Kasus T, Huleihel M, Liao C, Sun G, Nicklaus MC, Deschamps JR, Parrish DA, Marquez VE.
Sculpting the Bicyclo[3.1.0]hexane Template of Carbocyclic Nucleosides to Improve Recognition by Herpes Thymidine Kinase.
J Am Chem Soc. 129: 6216-6222, 2007.
[Journal]
46)  Liao C, Karki RG, Marchand C, Pommier Y, Nicklaus MC.
Virtual screening application of a model of full-length HIV-1 integrase complexed with viral DNA.
Bioorg Med Chem Lett. 17: 5361-5, 2007.
[Journal]
47)  Choi WJ, Shi ZD, Worthy KM, Bindu L, Karki RG, Nicklaus MC, Fisher RJ, Burke TR.
Application of azide-alkyne cycloaddition 'click chemistry' for the synthesis of Grb2 SH2 domain-binding macrocycles.
Bioorg. Med. Chem. Lett. 16: 5265-9, 2006.
[Journal]
48)  Zhao XZ, Semenova EA, Liao C, Nicklaus M, Pommier Y, Burke TR.
Biotinylated biphenyl ketone-containing 2,4-dioxobutanoic acids designed as HIV-1 integrase photoaffinity ligands.
Bioorg. Med. Chem. 14: 7816-25, 2006.
[Journal]
49)  Richard AM, Gold LS, Nicklaus MC.
Chemical structure indexing of toxicity data on the internet: Moving toward a flat world.
Curr Opin Drug Discov Devel. 9: 314-325, 2006.
Full Text Article. [Journal]
50)  Filippov I, Sitzmann M, Ihlenfeldt W, Nicklaus M.
Chemicals and Chemoinformatics Tools and User Services.
CADD Group Web Server. 0, 2006.
Full Text Article. [Journal]
51)  Kang JH, Benzaria S, Sigano DM, Lewin NE, Pu Y, Peach ML, Blumberg PM, Marquez VE.
Conformationally constrained analogues of diacylglycerol. 26. Exploring the chemical space surrounding the C1 domain of protein kinase C with DAG-lactones containing aryl groups at the sn-1 and sn-2 positions.
J. Med. Chem. 49: 3185-203, 2006.
[Journal]
52)  Song YL, Peach ML, Roller PP, Qiu S, Wang S, Long YQ.
Discovery of a novel nonphosphorylated pentapeptide motif displaying high affinity for Grb2-SH2 domain by the utilization of 3'-substituted tyrosine derivatives.
J. Med. Chem. 49: 1585-96, 2006.
[Journal]
53)  Pu Y, Peach ML, Garfield SH, Wincovitch S, Marquez VE, Blumberg PM.
Effects on ligand interaction and membrane translocation of the positively charged arginine residues situated along the C1 domain binding cleft in the atypical protein kinase C isoforms.
J. Biol. Chem. 281: 33773-88, 2006.
[Journal]
54)  Baleja JD, Cherry JJ, Liu Z, Gao H, Nicklaus MC, Voigt JH, Chen JJ, Androphy EJ.
Identification of inhibitors to papillomavirus type 16 E6 protein based on three-dimensional structures of interacting proteins.
Antiviral Res. 72: 49-59, 2006.
[Journal]
55)  Jiang S, Li P, Peach ML, Bindu L, Worthy KW, Fisher RJ, Burke TR, Nicklaus M, Roller PP.
Structure-based design of potent Grb2-SH2 domain antagonists not relying on phosphotyrosine mimics.
Biochem. Biophys. Res. Commun. 349: 497-503, 2006.
[Journal]
56)  Oishi S, Shi ZD, Karki RG, Worthy KM, Bindu L, Chertov O, Esposito D, Frank P, Gillette WK, Maderia M, Barchi Jr JJ, Nicklaus MC, Hartley J, Fisher RJ, Burke Jr TR.
Shimohigashi Y, eds.
Application of beta-branched allylglycine equivalents to macrocyclic Grb2 SH2 domain-binding inhibitors. In: Peptide Science 2004.
Osaka: The Japanese Peptide Society; 2005. p. 123-126 [Book Chapter]
57)  Oishi S, Kang UK, Karki RG, Worthy KM, Bindu L, Chertov O, Esposito D, Frank P, Gillette WK, Nicklaus MC, Hartley J, Fisher RJ, Burke Jr TR.
Shimohigashi Y, eds.
Synthesis and application of novel phosphotyrosyl mimetics to Grb2 SH2 domain-binding inhibitors. In: Peptide Science 2004.
Osaka: The Japanese Peptide Society; 2005. p. 397-400 [Book Chapter]
58)  Kang S, Shi Z, Karki R, Phan J, Worthy KM, Bindu LK, Nicklaus M, Waugh DS, Fisher RJ, Burke Jr TR.
Blondelle SE, eds.
Application of phenylphosphate mimetics to the design and synthesis of olefin metathesis-derived Grb2 SH2 domain-binding macrocycles. In: Understanding Biology Using Peptides.
La Costa, CA: American Peptide Society; 2005. p. 180-181 [Book Chapter]
59)  Liu F, Oishi S, Karki R, Shi Z, Worthy KM, Bindu LK, Maderia M, Nicklaus M, Barchi Jr JJ, Fisher RJ, Burke Jr TR.
Blondelle SE, eds.
High affinity Grb2 SH2 domain-binding macrocycles derived from ring-closing methathesis of alkenylglycine residues with beta-vinyl phosphotyrosyl mimetics. In: Understanding Biology Using Peptides.
La Costa, CA: American Peptide Society; 2005. p. 559-560 [Book Chapter]
60)  Burke TR, Kang S, Choi W, Shi Z, Karki RG, Phan J, Worthy KM, Bindu L, Nicklaus MC, Waugh D, Fisher RJ.
Application of phenylphosphate mimetics to the design and synthesis of olefin metathesisderived Grb2 SH2 domain-binding macrocycles.
Biopolymers. 80: 536, 2005.
[Journal]
61)  Kang JH, Peach ML, Pu Y, Lewin NE, Nicklaus MC, Blumberg PM, Marquez VE.
Conformationally constrained analogues of diacylglycerol (DAG). 25. Exploration of the sn-1 and sn-2 carbonyl functionality reveals the essential role of the sn-1 carbonyl at the lipid interface in the binding of DAG-lactones to protein kinase C.
J Med Chem. 48: 5738-48, 2005.
[Journal]
62)  Oishi S, Karki RG, Kang SU, Wang X, Worthy KM, Bindu LK, Nicklaus MC, Fisher RJ, Burke TR.
Design and synthesis of conformationally constrained Grb2 SH2 domain binding peptides employing alpha-methylphenylalanyl based phosphotyrosyl mimetics.
J Med Chem. 48: 764-72, 2005.
[Journal]
63)  Oishi S, Karki RG, Shi ZD, Worthy KM, Bindu L, Chertov O, Esposito D, Frank P, Gillette WK, Maderia M, Hartley J, Nicklaus MC, Barchi JJ, Fisher RJ, Burke TR.
Evaluation of macrocyclic Grb2 SH2 domain-binding peptide mimetics prepared by ring-closing metathesis of C-terminal allylglycines with an N-terminal beta-vinyl-substituted phosphotyrosyl mimetic.
Bioorg Med Chem. 13: 2431-8, 2005.
[Journal]
64)  Simmons DP, Peach ML, Friedman JR, Green MM, Nicklaus MC, De Luca LM.
Evidence that sequence homologous region in LRAT-like proteins possesses anti-proliferative activity and DNA binding properties: translational implications and mechanism of action.
Carcinogenesis. 27: 693-707, 2005.
[Journal]
65)  Liu F, Oishi S, Karki RG, Shi Z, Worthy KM, Bindu L, Maderia M, Nicklaus MC, Barchi JJ, Fisher RJ, Burke TR.
High affinity Grb2 SH2 domain-binding macrocycles derived from ring-closing metathesis of alkenylglycine residues with beta-vinyl phosphotyrosyl mimetics.
Biopolymers. 80: 574, 2005.
[Journal]
66)  Williams KL, Zhang Y, Shkriabai N, Karki RG, Nicklaus MC, Kotrikadze N, Hess S, Le Grice SF, Craigie R, Pathak VK, Kvaratskhelia M.
Mass Spectrometric Analysis of the HIV-1 Integrase-Pyridoxal 5'-Phosphate Complex Reveals a New Binding Site for a Nucleotide Inhibitor.
J Biol Chem. 280: 7949-55, 2005.
[Journal]
67)  Karki RG, Tang Y, Burke TR, Nicklaus MC.
Model of full-length HIV-1 integrase complexed with viral DNA as template for anti-HIV drug design.
J Comput Aided Mol Des. 18: 739-60 [Vol. year: 2004], 2005.
[Journal]
68)  Sun G, Voigt JH, Marquez VE, Nicklaus MC.
PROSIT, an online service to calculate pseudorotational parameters of nucleosides and nucleotides.
Nucleosides Nucleotides Nucleic Acids. 24: 1029-32, 2005.
[Journal]
69)  Lung FT, Chang C, Chong M, Liou C, Li P, Peach ML, Nicklaus MC, Lou B, Roller PP.
Small nonphosphorylated Grb2-SH2 domain antagonists evaluated by surface plasmon resonance technology.
Biopolymers. 80: 628-635, 2005.
[Journal]
70)  Sun G, Nicklaus MC, Xie R.
Structure, stability, and NMR properties of lower fullerenes C38-C50 and azafullerene C44N6.
J Phys Chem A. 109: 4617-22, 2005.
[Journal]
71)  Shi ZD, Karki RG, Worthy KM, Bindu LK, Nicklaus MC, Fisher RJ, Burke TR.
Utilization of a common pathway for the synthesis of high affinity macrocyclic Grb2 SH2 domain-binding peptide mimetics that differ in the configuration at one ring junction.
Chem. Biodivers. 2: 447-56, 2005.
[Journal]
72)  Shi ZD, Karki RG, Oishi S, Worthy KM, Bindu LK, Dharmawardana PG, Nicklaus MC, Bottaro DP, Fisher RJ, Burke TR.
Utilization of a nitrobenzoxadiazole (NBD) fluorophore in the design of a Grb2 SH2 domain-binding peptide mimetic.
Bioorg Med Chem Lett. 15: 1385-8, 2005.
[Journal]
73)  Tamamura H, Sigano DM, Lewin NE, Peach ML, Nicklaus MC, Blumberg PM, Marquez VE.
Conformationally constrained analogues of diacylglycerol (DAG). 23. Hydrophobic ligand-protein interactions versus ligand-lipid interactions of DAG-lactones with protein kinase C (PK-C).
J Med Chem. 47: 4858-64, 2004.
[Journal]
74)  Xie RH, Bryant GW, Sun G, Nicklaus MC, Heringer D, Frauenheim T, Manaa MR, Smith VH, Araki Y, Ito O.
Excitations, optical absorption spectra, and optical excitonic gaps of heterofullerenes. I. C(60), C(59)N(+), and C(48)N(12): Theory and experiment.
J Chem Phys. 120: 5133-47, 2004.
[Journal]
75)  Marquez VE, Ben-Kasus T, Barchi JJ, Green KM, Nicklaus MC, Agbaria R.
Experimental and structural evidence that herpes 1 kinase and cellular DNA polymerase(s) discriminate on the basis of sugar pucker.
J Am Chem Soc. 126: 543-9, 2004.
[Journal]
76)  Sun G, Voigt JH, Filippov IV, Marquez VE, Nicklaus MC.
PROSIT: Pseudo-Rotational Online Service and Interactive Tool, Applied to a Conformational Survey of Nucleosides and Nucleotides.
J Chem Inf Comput Sci. 44: 1752-62, 2004.
[Journal]
77)  Liu DG, Gao Y, Voigt JH, Lee K, Nicklaus MC, Wu L, Zhang ZY, Burke TR.
Acylsulfonamide-containing PTP1B inhibitors designed to mimic an enzyme-bound water of hydration.
Bioorg Med Chem Lett. 13: 3005-7, 2003.
[Journal]
78)  Zhang X, Pais GC, Svarovskaia ES, Marchand C, Johnson AA, Karki RG, Nicklaus MC, Pathak VK, Pommier Y, Burke TR.
Azido-Containing aryl beta-Diketo acid HIV-1 integrase inhibitors.
Bioorg Med Chem Lett. 13: 1215-9, 2003.
[Journal]
79)  Sigano DM, Peach ML, Nacro K, Choi Y, Lewin NE, Nicklaus MC, Blumberg PM, Marquez VE.
Differential binding modes of diacylglycerol (DAG) and DAG lactones to protein kinase C (PK-C).
J Med Chem. 46: 1571-9, 2003.
[Journal]
80)  Marchand C, Johnson AA, Karki RG, Pais GC, Zhang X, Cowansage K, Patel TA, Nicklaus MC, Burke TR, Pommier Y.
Metal-dependent inhibition of HIV-1 integrase by beta-diketo acids and resistance of the soluble double-mutant (F185K/C280S).
Mol Pharmacol. 64: 600-9, 2003.
[Journal]
81)  Poroikov VV, Filimonov DA, Ihlenfeldt WD, Gloriozova TA, Lagunin AA, Borodina YV, Stepanchikova AV, Nicklaus MC.
PASS biological activity spectrum predictions in the enhanced open NCI database browser.
J Chem Inf Comput Sci. 43: 228-36, 2003.
[Journal]
82)  Choi Y, Sun G, George C, Nicklaus MC, Kelley JA, Marquez VE.
Synthesis and conformational analysis of a locked analogue of carbovir built on a bicyclo[3.1.0]hex-2-enyl template.
Nucleosides Nucleotides Nucleic Acids. 22: 2077-91, 2003.
[Journal]
83)  Ihlenfeldt WD, Voigt JH, Bienfait B, Oellien F, Nicklaus MC.
Enhanced CACTVS browser of the Open NCI Database.
J Chem Inf Comput Sci. 42: 46-57, 2002.
[Journal]
84)  Strumberg D, Nitiss JL, Dong J, Walker J, Nicklaus MC, Kohn KW, Heddle JG, Maxwell A, Seeber S, Pommier Y.
Importance of the fourth alpha-helix within the CAP homology domain of type II topoisomerase for DNA cleavage site recognition and quinolone action.
Antimicrob Agents Chemother. 46: 2735-46, 2002.
[Journal]
85)  Neamati N, Lin Z, Karki RG, Orr A, Cowansage K, Strumberg D, Pais GC, Voigt JH, Nicklaus MC, Winslow HE, Zhao H, Turpin JA, Yi J, Skalka AM, Burke TR, Pommier Y.
Metal-dependent inhibition of HIV-1 integrase.
J Med Chem. 45: 5661-70, 2002.
[Journal]
86)  Nacro K, Sigano DM, Yan S, Nicklaus MC, Pearce LL, Lewin NE, Garfield SH, Blumberg PM, Marquez VE.
An optimized protein kinase C activating diacylglycerol combining high binding affinity (Ki) with reduced lipophilicity (log P).
J Med Chem. 44: 1892-904, 2001.
[Journal]
87)  Voigt JH, Bienfait B, Wang S, Nicklaus MC.
Comparison of the NCI open database with seven large chemical structural databases.
J Chem Inf Comput Sci. 41: 702-12, 2001.
[Journal]
88)  Lee J, Han KC, Kang JH, Pearce LL, Lewin NE, Yan S, Benzaria S, Nicklaus MC, Blumberg PM, Marquez VE.
Conformationally constrained analogues of diacylglycerol. 18. The incorporation of a hydroxamate moiety into diacylglycerol-lactones reduces lipophilicity and helps discriminate between sn-1 and sn-2 binding modes to protein kinase C (PK-C). Implications for isozyme specificity.
J Med Chem. 44: 4309-12, 2001.
[Journal]
89)  Marquez VE, Wang P, Nicklaus MC, Maier M, Manoharan M, Christman JK, Banavali NK, Mackerell AD.
Inhibition of (cytosine C5)-methyltransferase by oligonucleotides containing flexible (cyclopentane) and conformationally constrained (bicyclo[3.1.0]hexane) abasic sites.
Nucleosides Nucleotides Nucleic Acids. 20: 451-9, 2001.
[Journal]
90)  Ford H, Dai F, Mu L, Siddiqui MA, Nicklaus MC, Anderson L, Marquez VE, Barchi JJ.
Adenosine deaminase prefers a distinct sugar ring conformation for binding and catalysis: kinetic and structural studies.
Biochemistry. 39: 2581-92, 2000.
[Journal]
91)  Chen IJ, Neamati N, Nicklaus MC, Orr A, Anderson L, Barchi JJ, Kelley JA, Pommier Y, MacKerell AD.
Identification of HIV-1 integrase inhibitors via three-dimensional database searching using ASV and HIV-1 integrases as targets.
Bioorg Med Chem. 8: 2385-98, 2000.
[Journal]
92)  Mu L, Sarafianos SG, Nicklaus MC, Russ P, Siddiqui MA, Ford H, Mitsuya H, Le R, Kodama E, Meier C, Knispel T, Anderson L, Barchi JJ, Marquez VE.
Interactions of conformationally biased north and south 2'-fluoro-2', 3'-dideoxynucleoside 5'-triphosphates with the active site of HIV-1 reverse transcriptase.
Biochemistry. 39: 11205-15, 2000.
[Journal]
93)  Wang PY, Brank AS, Banavali NK, Nicklaus MC, Marquez VE, Christman JK, MacKerell AD.
Use of Oligodeoxyribonucleotides with Conformationally Constrained Abasic Sugar Targets to Probe the Mechanism of Base Flipping by HhaI DNA (Cytosine C5)-methyltransferase.
J Am Chem Soc. 122: 12422-12434, 2000.
[Journal]
94)  Marquez VE, Russ P, Alonso R, Siddiqui MA, Shin KJ, George C, Nicklaus MC, Dai F, Ford H.
Conformationally restricted nucleosides. The reaction of adenosine deaminase with substrates built on a bicyclo[3.1.0]hexane template.
Nucleosides Nucleotides. 18: 521-30, 1999.
[Journal]
95)  Strumberg D, Nitiss JL, Rose A, Nicklaus MC, Pommier Y.
Mutation of a conserved serine residue in a quinolone-resistant type II topoisomerase alters the enzyme-DNA and drug interactions.
J Biol Chem. 274: 7292-301, 1999.
[Journal]
96)  Marquez VE, Russ P, Alonso R, Siddiqui MA, Hernandez S, George C, Nicklau MC, Dai F, Ford H.
Synthesis of Conformationally Restricted Carbocyclic Nucleosides: The Role of the O(4')-Atom in the Key Hydration Step of Adenosine Deaminase.
Helvetica Chimica Acta. 82: 2119-2129, 1999.
[Journal]
97)  Dirk S, Nitiss J, Dong J, Nicklaus M, Kohn K, Heddle J, Maxwell A, Pommier Y.
The Third Alpha-helix of the CAP Homology Domain of Type H Topoisomerases is Critical for DNA Cleavage Site Recognition and Quinolone-action.
Clin Cancer Res. 5: 670-, 1999.
[Journal]
98)  Nicklaus MC, Williams RW, Bienfait B, Billings ES, Hodoscek M.
Computational chemistry on commodity-type computers.
J Chem Inf Comput Sci. 38: 893-905, 1998.
[Journal]
99)  Milne GW, Nicklaus MC, Wang S.
Pharmacophores in drug design and discovery.
SAR QSAR Environ Res. 9: 23-38, 1998.
[Journal]
100)  Nicklaus M.
Conformational Energies Calculated by the Molecular Mechanics Progam CHARMm.
J Comput Chem. 18: 1997, 1997.
[Journal]
101)  Neamati N, Hong H, Mazumder A, Wang S, Sunder S, Nicklaus MC, Milne GW, Proksa B, Pommier Y.
Depsides and depsidones as inhibitors of HIV-1 integrase: discovery of novel inhibitors through 3D database searching.
J Med Chem. 40: 942-51, 1997.
[Journal]
102)  Hong H, Neamati N, Wang S, Nicklaus MC, Mazumder A, Zhao H, Burke TR, Pommier Y, Milne GW.
Discovery of HIV-1 integrase inhibitors by pharmacophore searching.
J Med Chem. 40: 930-6, 1997.
[Journal]
103)  Nicklaus MC, Neamati N, Hong H, Mazumder A, Sunder S, Chen J, Milne GW, Pommier Y.
HIV-1 integrase pharmacophore: discovery of inhibitors through three-dimensional database searching.
J Med Chem. 40: 920-9, 1997.
[Journal]
104)  Wang S, Milne GW, Yan X, Posey IJ, Nicklaus MC, Graham L, Rice WG.
Discovery of novel, non-peptide HIV-1 protease inhibitors by pharmacophore searching.
J Med Chem. 39: 2047-54, 1996.
[Journal]
105)  Milne GW, Wang S, Nicklaus MC.
Molecular modeling in the discovery of drug leads.
J Chem Inf Comput Sci. 36: 726-30, 1996.
[Journal]
106)  Nicklaus MC, Ford H, Hegedus L, Milne WA, Kelley JA.
Comparative molecular field analysis of hydrophobicity descriptors of cytosine nucleosides.
Quant Struct-Act Rel. 14: 335-343, 1995.
[Journal]
107)  Nicklaus MC, Wang S, Driscoll JS, Milne GW.
Conformational changes of small molecules binding to proteins.
Bioorg Med Chem. 3: 411-28, 1995.
[Journal]
108)  Marquez VE, Jeong LS, Nicklaus MC, George C.
Synthesis and Biological-Activity of Sugar-Fluorinated 2',2'-Dideoxy-4'-thioribofuranosyl Nucleosides.
Nucleosides & Nucleotides. 14: 555-558, 1995.
[Journal]
109)  Rodriguez JB, Marquez VE, Nicklaus MC, Mitsuya H, Barchi JJ.
Conformationally locked nucleoside analogues. Synthesis of dideoxycarbocyclic nucleoside analogues structurally related to neplanocin C.
J Med Chem. 37: 3389-99, 1994.
[Journal]
110)  Jeong LS, Nicklaus MC, George C, Marquez VE.
Down Hydroxyl Groups - Retention of Configuration after Fluoride Opening of the Quaternized N-3-MEM Anhydronucleotides.
Tet Lett. 35: 7573-7576, 1994.
[Journal]
111)  Milne GW, Nicklaus MC, Driscoll JS, Wang S, Zaharevitz D.
National Cancer Institute Drug Information System 3D database.
J Chem Inf Comput Sci. 34: 1219-24, 1994.
[Journal]
112)  Wang S, Milne GW, Nicklaus MC, Marquez VE, Lee J, Blumberg PM.
Protein kinase C. Modeling of the binding site and prediction of binding constants.
J Med Chem. 37: 1326-38, 1994.
[Journal]
113)  Jeong LS, Nicklaus MC, George C, Marquez VE.
Unanticipated Retention of Configuration in the Dast Fluorination of Deoxy-4'-Thiopyrimidine Nucleosides with Up Hydroxyl Groups.
Tet Lett. 35: 7569-7572, 1994.
[Journal]
114)  Nicklaus MC, Milne GW, Zaharevitz D.
Chem-X and CAMBRIDGE. Comparison of computer generated chemical structures with X-ray crystallographic data.
J Chem Inf Comput Sci. 33: 639-46, 1993.
[Journal]
115)  Nicklaus MC, Milne GW, Zaharevitz D.
Concord and Cambridge - Comparison of Computer-Generated Chemical Structures with X-Ray Crystallographic Data.
J Chem Inf Comput Sci. 33: 155-163, 1993.
[Journal]
116)  Milne GWA, Nicklaus MC, Hodoscek M.
Molecular modeling in solvent.
J Mol Struct. 291: 89-103, 1993.
[Journal]
117)  Rodriguez JB, Marquez VE, Nicklaus MC, Mitsuya H, Barchi JJ.
Synthesis of Cyclopropane-fused Dideoxycarbocyclic Nucleosides Structurally Related to Neplanocin-C.
Tet Lett. 34: 6233-6236, 1993.
[Journal]
118)  Milne GW, Nicklaus MC.
Use of computer graphics in drug design.
NIDA Res Monogr. 134: 129-45, 1993.
[Journal]
119)  Nicklaus MC, Milne GW, Burke TR.
QSAR of conformationally flexible molecules: comparative molecular field analysis of protein-tyrosine kinase inhibitors.
J Comput Aided Mol Des. 6: 487-504, 1992.
[Journal]
Click Here to View Collapsed Bibliography.

This page was last updated on 9/13/2013.